Wednesday, August 20, 2014

Diversity metrics

I want to blog about two recently published papers, one on keys and one on a method for spatial analyses of biodiversity, but for the latter some groundwork is necessary. This post will provide that groundwork so that I can then cunningly link back to it.

The last 25 years or so have seen the rise of spatial studies of patterns of biodiversity. They have been made possible by the increased availability of large databases with specimen occurrence records such as Australia's Virtual Herbarium, for example. Where a generation ago most information on the occurrence of species came from distribution maps drawn by specialists on the various groups of organisms, we can now enter a species name into a database search and are rewarded by a large list of geocoded specimens ready for use in our analyses.

Over the same time, several new diversity metrics have been developed to allow ever more sophisticated analyses. What is a diversity metric? It is a numerical value that tells us how diverse the organisms of our study group are in a particular part of our study area.

The study area as a whole is divided into cells; ideally these are equal area cells of for example 100 km x 100 km, alternatively they are biogeographical or political units. We can then look at our diversity metric and say, aha, in this cell there is particularly high diversity, and that might influence our decisions about what areas to prioritise for conservation. Okay, now what metrics are there?

Tuesday, August 19, 2014

Botany picture #170: Banksia integrifolia

Banksia integrifolia (Proteaceae), Jervis Bay, 2014. This may be the best known Banksia, for a variety of reasons. First, it occurs the coast near Sydney where a lot of foreign tourists can see the species. Second, that also means that it was one of the first species of the genus ever to be collected by a European scientist, Joseph Banks himself. Third, it is an easily cultivated plant found as an ornamental tree or even Bonsai in various parts of Australia. And fourth, it has even been introduced to other countries, and there is slight concern that it might turn into an invasive weed in New Zealand.

As can be seen in the above picture, the flower spikes as well as the fruiting cones are very attractive.

Monday, August 18, 2014

A metric of Twitter and blog hits for scientific articles

On this blog I have sometimes mentioned, and complained about, the influence that the obsession with article citations and journal impact factors (IF) has on scientific publishing, scientific careers, and the hiring choices of scientific institutions.

In short, instead of actually reading and understanding scientific papers, many people 'assess' their value by looking at how often they have been cited. Instead of reading and understanding their work, many people, even members of search committees or advisors of funding agencies, 'assess' scientists by looking at how often their papers have been cited. And instead of reading and understanding the articles published in them, many people 'assess' scientific journals by looking at how often their average article is cited within the first two years after publication.

And as mentioned before, this approach systematically favours areas of science that have a quick turn-around and lots of practitioners able to cite each other whereas it systematically disadvantages areas of science where many publications are written for long term use, published in books as opposed to journals, and while very useful to many people may not even be meant to be cited. Such as the floras and monographs produced by taxonomists, for example.

But of course, once you think you know what bad looks like somebody will introduce you to something worse.

Saturday, August 16, 2014

Botany picture #169: Corymbia gummifera

Corymbia gummifera (Myrtaceae), Jervis Bay, 2014. Only slowly I am beginning to really appreciate the Myrtaceae family. I must admit that when I came here I decided to focus on learning other groups first, especially Asteraceae, Lamiaceae, Acacia and Proteaceae, but now I am starting to get a handle on the generic concepts in that family.

Corymbia is generally easily recognised by the attractive, urn-shaped capsules, as seen in this picture.

Thursday, August 14, 2014

In praise of PAUP*

Hell is freezing over! Pigs are flying! PAUP* is getting updated for the first time in twelve years!

Jokes aside, this is great news. PAUP*, short for Phylogenetic Analysis Using Parsimony (* and other methods), is one of the best known software tools for phylogenetics. Indeed to me it is pretty much the phylogenetic software tool. Yes, depending on the task at hand I also use TNT, RAxML, Mesquite, MrBayes and BEAST with various of its add-ons, but PAUP* is the one I started out with while writing my thesis and it is still the one I feel most comfortable using.

Another major issue is what you can and cannot do with the various programs. The downside of PAUP*, or at least of the previous version, is that it is comparatively slow. So if you have a large dataset with many taxa, you are better off using TNT for parsimony and RAxML for likelihood analyses. But PAUP* can do various kinds of analyses that no other software can do; for example, I would not know how to conduct a Templeton test without it.

(My experience with PHYLIP is limited. Maybe it can do some of the same things. The problem is that its combination of rather excessive modularity and a call centre style user interface - on the lines of "press 3 for this kind of analysis" - has put me off using it so far.)

So over the past few years I have sometimes worried about the day when PAUP* would suddenly stop working on the newest computers. It is good to know that a new version is coming up!

The idea is that ultimately there will be GUIs for Win and Mac that one has to buy, but that command line versions for Win, Mac and Linux will be free. I guess I will be happy to use command line myself, but it might be a good idea to get a GUI licence for small student projects where the student cannot necessarily be expected to learn the PAUP* commands.

Wednesday, August 13, 2014

Effective altruism: earning to give

Until recently, I was only marginally aware of the Effective Altruism Movement, but after reading a somewhat odd blog post from one of its proponents, Chris Hallquist, I decided to at least look up the Wikipedia article. It summarises the principles of the movement as follows (accessed 13 August 2014):
  • Cost-effectiveness: Effective Altruists (EAs) aim to make donations where they will work the greatest good per unit of currency spent. Although I found Wikipedia's remark that "many effective altruists have backgrounds in philosophy, economics, or mathematics, fields that involve rational and quantitative thinking" rather puzzling because I don't think that economists are necessarily rational (or good at empiricism for that matter), working out where the greatest difference can be made is surely something that everybody should be able to get behind.
  • Cause prioritisation: This is similar to the first point, in that EAs think hard about what charitable causes are the worthiest. Again, in principle this should make sense to anybody, but the obvious problem is that opinions about what should be prioritised differ. Wikipedia tells us, "most effective altruists think that the most important causes to focus on are currently poverty in the developing world, the suffering of animals on factory farms, and humanity's long term future." In my eyes, the second one should be a couple dozen levels of priority behind the first one, and if it is indeed seen as a serious problem then it could quite simply be addressed by making a law that forbids factory farms. The third cause needs clarification: what is meant here? For example, Hallquist appears to be one of those who believe that the greatest risk humanity faces is that we develop an artificial superintelligence that will kill us all; I, on the other hand, consider the people who collect donations to "work on that problem" to be charlatans, and the money donated to them to be wasted. If, on the other hand, the money were put towards solving a real problem such as how to develop cheaper solar cells, then we'd be talking... But maybe that's just me.
  • Impartiality: all human lives have equal value, no matter how distant they are from us. That is a noble sentiment and should, of course, be a fundamental rule of every civilised society. But applied as an ethical guideline to individuals, as it would have to be in a decentralised charitable movement, it is unrealistic to the degree of being inhumane. Nobody can expect me to care as much about somebody I will never meet as about my own daughter, nor would I expect, say, a Norwegian teacher to care as much about me as she cares about her own sister. An ethical system that is utterly incompatible with human nature is a dubious proposition.
  • Donating to charity is morally required as opposed to merely laudable. Hm. I would rather prefer to construct society in such a way that everybody is cared for by the state, and thus not in need of charity in the first place. You can tell people that charity is a duty all you want but if times get tough they will still look after their own, and then a system that relies on charity will fail to help the weak.
  • Counterfactual reasoning: This is a bit of an odd name for what is going on here, and more importantly this is the kind of argument that got me hooked in the first place, so more below.
See, reading between the lines here EAs reject the idea that the best way to do charity is direct action, such as doing something charitable yourself. They argue that it is usually more efficient to (1) go into a high-paying job or lucrative business and earn loads of money, (2) give a part of that money to charity and (3) have the charity hire somebody else to do the charitable things for you. (In this point at least the influence of the aforementioned economists on the movement is plainly visible.)

That logic leads then to considerations such as this one where Hallquist weighs the hypothetical benefits of working in a high-paying job at Google against contributing to a technological start-up company and frames it as a question of charity.

This is where it occurred to me that the EA movement might actually not be that new a concept. Basically, it is like any rich comfortable people throughout history trying to soothe their conscience, with the only difference that EAs start working on that before they even got rich.

The question is, of course, whether trying to get rich does not contribute to precisely the things that they will afterwards have to put right with their donations. Of course they will not necessarily do anything as crass as investing in a company that is very profitable because it exploits its workers to the point where they commit suicide and then donating money to the widows and orphans, or working for a company that poisons a lake and then donating to the clean-up efforts. But even if their efforts at generating the greatest possible profit for charity are not as directly destructive as that, there is possibly some truth to the following poem from Bertold Brecht:
Reicher Mann und armer Mann
Standen da und sahn sich an.
Und der Arme sagte bleich:
Wär ich nicht arm, wärst Du nicht reich.
(Rich man and poor man stood and looked at each other. And the poor one said, if I wasn't poor you wouldn't be rich.)

After all, if the amount of money in an economy is kept constant, then for somebody to become richer somebody else must become poorer. If the amount is increased by money printing, as it must be if the economy is supposed to grow without experiencing destructive price deflation, then relative wealth still works as a zero sum game. For everybody who manages to become part of the 1% top earners somebody else has to drop out of that percentile.

I guess an Effective Altruist could tell themselves that if they get rich, and the person who gets less wealthy was somebody who did not give to charity, then the net effect is positive. But as this post will have shown, so far the logic of the movement does not entirely convince me. Its principles seem to be an odd combination of no-brainers, noble but misguided ethics, and thin justifications for careerism and profiteering.

All this, obviously, assuming that Wikipedia does a good job of summarising these principles. That is not a given, but one would hope that EAs have contributed to the article.

Monday, August 11, 2014

Bad systematics

On the recent field trip, I saw the weird pesticide below in the station:

As most readers will know, this is wrong in two distinct ways: First, flies are insects, so this is a bottle of insect and insect killer. Second, spiders are NOT insects. So why not rename the pesticide into "spider & insect killer"?

The little insect icons are pretty weird too. Note how all of them are merely sitting there - except the flea, which is depicted as dead with cracked eggs above it. I imagine the latter are supposed to indicate that the eggs are also killed, not only the imagines, and then the designers probably thought that drawing a sitting flea in the same box would somehow imply that the imagines are not killed.

Anyway, this "fly & insect" business reminds me of an anecdote from the time of my postgraduate studies. The head of our department, a liverwort specialist, wanted to hire a student to work on a database. From what I was told his approach to job interviews was as follows: He showed each candidate the database website which, at that moment, he deliberately given the title "bryophytes and liverworts". Apparently most candidates said merely that it looked nice. He hired the only one who immediately remarked that the title didn't make sense because one of those is a subgroup of the other.

Also on the field trip, one student collected a Lomandra. When I helped her with the identification of the species, I quickly despaired of the key we were using. Don't want to mention names here, but the questions were often unhelpful; the worst of them was probably this one:

3  Male inflorescence usually unbranched; female inflorescence unbranched or rarely branched.
3* Male inflorescence branched; female inflorescence branched or unbranched.

So basically, unless you have an unbranched male inflorescence on your specimen (and she didn't) the couplet is useless; if it is branched, you have to try both ways, and the text about the female inflorescences is entirely uninformative. When the taxonomist wrote that, didn't they realise what they were doing?